Researching Creation

August 28, 2010

Biological Change / Random Thought on Diversification

Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes.

While arabidopsis is probably a different created kind than rice, it got me wondering - what if, when two species enter into symbiosis, one species transfers pseudogenes to another, which are then used in gene conversion to set up the biochemical pathways for the symbiosis?

Thus, pseudogenes might act like a symbiosis integration script, giving a template for interacting with it. The other organism then takes that template, and, through gene conversion, uses pieces out of it to alter its own genome to match the symbiosis?

May 05, 2010

Biological Change / The Cognitum, Pt. 1

JB

The "cognitum" is a concept in creation taxonomy that groups animals according to the perceptions that humans have about those creatures. I have been a fan of the idea of the cognitum since I first heard about it from Sanders and Wise's paper at ICC. The goal is to develop a standard of taxonomy based specifically on human perception, and not at all on other standards such as genetic data or morphology.

I found this idea extremely intuitive. There is obviously the Biblical reason that Adam was given to naming each kind that God created. Therefore, perhaps God gave Adam (and by extension the rest of us) the power to discern important relationships. It is interesting, for instance, that even children can usually tell, from a simple drawing, the difference between a cat and a dog, despite their relatively similar morphology, combined with the simpleness of the drawing. The same child can, at least by Sanders and Wise's paper, look at a more bizarre representative of the cat family and still identify it as a cat.

But, I think there is another point worth looking at. When there is a debate about the phylogeny of a species on whether it should be grouped according to its morphology vs. its DNA sequences, how is such a decision decided (or for that matter, when any two trees are in conflict)? I think few people think about how tough a question this is. No one saw the type of animals who were the current animals' ancestor. Therefore, we must lean on secondary evidence. But if the secondary evidence is in conflict, there seems to be some sort of a faculty in the human mind that makes such discernments. It is neither perfect nor consistent, but nonetheless it is there.

Sanders and Wise's paper has a whole host of interesting points:

Most taxonomies (scientific or folk) have animals which are at a "fuzzy boundary" - that is, they "kind of" belong to one or more other groups, but have features that separate them quite significantly. Paleoherbs, for instance, have a mixture of features from the two main groups of flowering plants - monocots and dicots, and so are in the fuzzy boundary

The idea of the fuzzy boundary allows us to apply fuzzy-set theory to biosystematics

Classification is an important part of human experience

Most lay people can recognize multiple species as belonging to the same general type, even in somewhat more difficult cases

Most societies employ four or five hierarchical levels of taxonomy, utilize only the outermost levels for their naming, and reserve the fifth level of taxonomy for minor variants. This is interesting if one considers the true distinct "kinds" to exist at these levels of naming, and not at the higher ones.

The cat family, for instance, seems to be a holobaramin, yet certain other animals (meercats and hyaenas) elicit a distinct "felid" response from humans. Why is that?

Species probably expanded to fill a pre-defined biological character space, which is one way God communicates His design to humans

The adaptive radiation and refilling of the earth after the flood to fill biological character space probably produced some overlap from different groups

As part of understanding God's design, we should examine how far the parts of God's design can be modified without disrupting the "gestalt" pattern that is recognizable.

We can compare the underlying functions associated with an organism's "gestalt" with the variation of functions present within a cognitum

The cognitum concept lies in continuity with the platonic view of biology which predominated the pre-Darwinian era. Creationists should revisit many of these taxonomical concepts to see which ones we need to incorporate into the modern Creation viewpoint.

With the cognitum concept in mind, we should evaluate the genetic basis of different patterns and identify the genomic constraints that restrict the distribution of patterns

How and why are larger cognita chained together by a fuzzy boundary?

Is there some line after which fuzzy boundaries give way to clear-cut phylogeny? Might this help draw the line for baramins?

Hopefully, as the cognitum concept is studied we will learn to differentiate homoplasy (cross-line similarity) due to separate origins from homoplasy from genetic recombination within the same cognitum.

We need to look into the cognitive neuroscience of gestalt formation in the human mind

Is there a relationship between human memory capacity and the structure of the biological world (i.e. so that humans can comprehend it)

Cognita could be used to identify basic baramins and inclusions for baramins before we have a good breeding/morphological/genetic analysis

Anyway, as you can see, there were a lot of things that jumped out at me.

I also had a thought - I wonder if the "fuzzy boundary" organisms might have originated in locations with a low diversity of species. So, basically, an organism "sensed" the lack of biological character space, and then morphed to fill it.

It is interesting to compare this notion of taxonomy with a study on <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635482/?tool=pubmed">adaptive radiations in cichlid fish</a>. I have not read it in detail (a commenter on UD pointed me to it), but the abstract says, "The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5Myr into a radiation speciation becomes a lot less frequent."

But even more interesting is this statement -- "The available data suggest that the propensity to undergo adaptive radiation in lakes evolved sequentially along one branch in the phylogenetic tree of African cichlids, but is completely absent in other lineages."

This indicates that there might be a "basal-type" species which is presumably more similar to ark-based species than others, from whom adaptive radiations tend to take place. This would be super-awesome if it is true.

What is most striking from the results compiled in Appendix A is the high level of support by the molecular data for the circumscription of the core groups of most of the primary cognita identified. ... This suggests that the core groups of primary cognita are units that are generally internally consistent morphologically, as well as genomically. ... The decoupling of molecular similarities from morphological similarities just above the family/order level suggests that the circumscribed core groups of cognita at this level or the subfamily/family level may closely reflect the constitution of holobaramins represented by them. In fact, more precise methods of documenting both the decoupling of morphological and molecular characters and mosaic recombination of these characters, so easily depicted in a cognitum system, may eventually prove to serve as a criterion in delimiting holobaramins.

February 10, 2010

Biological Change / Randomness in Creation

JB

About two years ago I got my first major paper published in the Creation Research Society Quarterly. You can read a summary of it here. Today, I received permission to post the paper publicly on my website! Yay! If you are interested, check out the paper:

January 07, 2010

Tiktaalik has dominated a lot of the media discussion about evolution in the last few years. For those who don't know, Tiktaalik is a fossil "fish-o-pod" found in Canada, that is claimed to be an "intermediate form" between fish and early tetrapods (tetrapods are four-limbed creatures). In addition, it was claimed that it was in the evolutionary-correct position in the fossil record for the fish-tetrapod transition (late Devonian).

Now, the basic problem in Tiktaalik is that it isn't "transitional" so much as mosaic - that is, it has features of "earlier" and "later" creatures, but no features that might be considered "in transition". Each feature that it has, it has fully. This indicates that, if it did "evolve", it did so non-Darwinistically - that is, the information seems to have already been in the gene pool, and was merely activated. On the other hand, in absense of a mechanism of macroevolution, there is no reason to think that it evolved at all. And from a flood geology perspective it gets even more interesting, but I'll leave that for the moment.

In addition to all this, there is a certain kind of criticism that emerges from lay people that you don't tend to find among experts. That criticism is of the form of "is this really all the information there is? Does it really add up the way you say it does? Is it not possible that there is other evidence out there that you just haven't found yet - perhaps because you weren't looking for it?"

Now, this kind of criticism is usually just ignored by experts, but I personally think that it is epistemologically valid, and an important part of public discourse. The fact is, every discipline needs to be confident in its own ability to find truth. However, equally important, is that the public should not grant each discipline the same amount of credulity that it grants for itself. A discipline can't go anywhere if it has to spend all its days proving its assumptions. On the other hand, if you can't prove your assumptions fully, then your findings are not binding on others. If someone has a larger worldview, then different aspects may be in competition. Why should a person give up belief X which is important to them and which they believe they hold validly, when they don't agree with the assumptions of contradictory belief Y, especially if it is relatively unimportant to their daily lives?

What they found is, according to evolutionary timescales, a full-fledged tetrapod existed about 20 MILLION years prior to Tiktaalik. While Tiktaalik was a transitional, this thing was fully-tetrapod. So, this blows any story about Tiktaalik and evolution completely out of the water. Tiktaalik has nothing to do with the evolution of tetrapods, because, if evolution is correct, full-blown tetrapods predated the transitional species by about 20 million years.

It's dangerous to put your faith in circumstantial evidence, because the facts can change that quickly. Yesterday it was an open-and-shut case for Tiktaalik being found right where it was supposed to be in evolutionary transition. Today, it is more than 20 million years out-of-date. I say "more than" because, according to evolutionary theory, the tetrapods would have still required time to evolve before this creature existed.

So here's where it gets really interesting - the new find is footprints. Here's a few things that don't usually get a large mention in introductory textbooks:

There are large gaps (sometimes a hundred million years) in the fossil record where a given species must have existed but did not leave any fossils. Two examples are the Wollemi pine and the Coelacanth. These were last seen in the fossil record 150 and 65 million years ago, respectively, yet they still live today.

Many measures of the fossil record show that it is relatively complete

Most creatures are first known from trace fossils (i.e. footprints or other types of trackways) long before we ever see their body fossils.

The interesting implication of #1 is that there is NO WAY AT ALL to infer from the fossil record how long something has been in existence. If we can verify that the fossil record can be off 100 million years in one direction, if we assume that the same thing can happen in the other direction, then that means that you have a possible margin of error of about half of the phanerozoic era (the phanerozoic is the complete fossil-bearing section of the fossil record). How can you possibly have a detailed evolutionary progression when you can have this kind of discrepancy between fossil evidence and reality? If the best you can do is establish which half of the geologic column they existed in, how good is your data, and how are you going to derive evolutionary expectations from it?

Let's look at the second idea - that the fossil record actually seems complete. There are many ways of measuring completeness. The interesting thing is that most of them point to the fossil record being essentially complete, at least to the biological "family" level. That doesn't mean that we won't find anything new, just that we've probably found more than we haven't. So, this makes an interesting corrective to the preceding paragraph. Maybe the completeness of the fossil record gives us confidence that most of the extents of organisms are well-represented in the fossil record, and these two (and some others) are merely anomalies. That could almost work, except...

Trace fossils — footprints, trackways or trails — are fascinating but often frustrating sources of information. Body fossils of the track makers almost never occur in the same rock beds, so complicating interpretation.

It is much harder to preserve a trackway than a bone. So why do we know most organisms by trace fossils before we know them as body fossils, and why are the two rarely found in the same rock beds?

In this paper, Brand and Florence argue that the reason for this is that it evidences fleeing behavior. The flood didn't happen all at once. It waxed and waned until it covered the earth, which didn't happen until day 150. Until then, the increasing floods would still have had tides from the moon, and gone in and out over increasing landmasses. Therefore, if there is a footprint, it is probably of a living creature, not a drowning one. If there is a body fossil, it is probably a drowned creature. So if the waters had temporarily receded, new trackways could be lain. When the waters come back and deposit a new layer, they are killing off organisms into a different rock bed.

In any case, this is getting to be rambling. My main point is that this new fossil find has very interesting implications for both creationists and evolutionists, and tends to validate thought-patterns of lay critics of evolution.

UPDATE:

I wrote this last night but forgot to publish it. In the meantime, several other people have chimed in on the new tracks:

David Coppedge gives nice pull-quotes from several news sources, and points out that the researchers noted that many tracks in even older sediments may have been misinterpreted, and may be tetrapods as well. One thing that is interesting to note is that these older tracks have been with us the whole time, and the reason they were not interpreted as tetrapods is that tetrapods weren't expected to have been alive at that time. It is always fascinating the ways that our minds work - in many cases only by believing in the credibility of something beforehand are we able to find the evidence that supports that.

January 06, 2010

Biological Change / ID in Scientific Literature

JB

A recent development has been that some science journals are now publishing papers that deal with Intelligent Design. Unfortunately, at least so far, they are only looking at the perspectives of the anti-IDists. Most journals, when someone's idea is specifically being attacked, take the courtesy to alllow that person to respond, but so far that courtesy has not extended to IDists.

Nonetheless, it is interesting that ID has actually moved up the scale to the point where the journals realize that they have to grapple with these subjects at least a little bit.

One example is the Journal of Eukaryotic Microbiology which recently published the paper, "Using Protistan Examples to Dispel the Myths of Intelligent Design". The paper basically argues against Meyer's use of the Cambrian explosion as a launchpad for ID-based criticism of Darwinian evolution, and Behe's use of chloroquine-resistance for setting the limits of Darwinian evolution.

While the paper brings out several good points, the fact that the problems pointed out were so few and much to the side of the issue is contrasted with the name-calling they engage in, saying that Behe "demonstrates extraordinarily bad scholarship".

Let me make this clear - NO MATTER WHAT YOUR POSITION IS, BEING WRONG IS NOT EQUIVALENT WITH BAD SCHOLARSHIP. And there is NOWHERE in the paper where they level any charge against Behe which would be considered bad scholarship. They showed that there was a paper contraindicative of his findings that was published two years before his book. So what? People miss papers all the time, some of theme intentionally so because they are bad. Sometimes accidentally, considering the massive numbers of papers published every day. Simply leaving out a paper and disagreeing with people is not bad scholarship. Nor is publishing in books when a journal won't give you a fair hearing. In addition, they characterized Behe's detailed responses to criticism as "brushing them off". There is such a thing as a brush-off response. Behe's "Waiting Longer for Two Mutations" is no such thing.

It's pretty sad that, rather than arguing over the general thesis of Behe's work - that transformations which require multiple simultaneous amino acid changes are nearly impossible by Darwinian mechanisms - they instead argue over whether chloroquine requires multiple simultaneous mutations. This is missing the forrest because of the trees. If their point was to criticize chloroquine-resistance as a base reference for the limits of evolvability, it was a decent paper. If their point was, instead, to show that the ID project itself is misguided, they showed nothing of the sort. The fact that they engaged in such namecalling throughout the paper simply made the paper a sad reflection on the state of science today.

The paper deals with other ideas as well, and possibly I will have time later to get into them.

December 03, 2009

Biological Change / Putting Mutations in Context

Using Creation Theory to Explore Biology

JB

I thought I would direct your attention to my latest paper, Towards a Creationary Classification of Mutations. The goal of this paper is to get beyond defining whether or not a mutation is beneficial or not, and looking into whether or not the mutation is part of a larger genomic architecture. I include the outline of an experimental methodology which could be used to evaluate this. I would love any feedback you have on the paper, especially if you can think of additional criteria to consider, and/or additional experimental methods that could be used to evaluate these criteria.

My hope is to help make Creation a help to biologists doing experimental work, rather than just a claim to be justified. I believe truly that God is the foundation of knowledge, and that we can put the concepts of creation to work in exploring biology. So, my hope is to outline ways in which creation can aid in this exploration.

November 29, 2009

Biological Change / On-the-fly Untemplated Protein Modifications

JB

A HUGE new discovery - it appears that cells can react to cell stresses, and then start building modified proteins to account for the stress. These modifications are not genetically coded.

In the specific test case, cells reacted to the presence of reactive oxygen species (ROS) by adding methionines into proteins at various locations to protect the protein's function. The sulfur in methionine helps protect against ROS in the cell.

October 11, 2009

I've been on quite a gardening kick lately, and one of the things I have been growing is tomatoes. I am growing several different heirloom tomatoes, and none of them want to ripen on the vine. Either that, or being ripe on the vine is what is attracting all the bunnies to eat them. In any case, I have to pick them while they are still green.

Well, my last two batches of tomatoes decided that they didn't want to ripen up. They just wanted to stay green. Now, I know that Fried Green Tomatoes is a classic southern dish, but that just takes too much work and is too much of a mess. So, I decided to try drying them. I just sliced them up, stuck them on a rack with a little salt, and stuck them in the oven @ 225°F for a few hours. They tasted delicious. There's only one problem - many people think that green tomatoes are poisonous.

This is because they are part of the Solanum genus (nightshades). Solanums have a type of chemical in them called alkaloids, the most famous of which is probably Solanine. This substance is neurotoxic to humans. Many people say that green tomatoes shouldn't be eaten in medium or large quantities because of the large amounts of solanine in them (but ripe, red tomatoes are fine because the solanine gets catabolized during ripening).

So, curious as to whether I was creating a toxic hazard or an edible treat, I decided to do some digging. What I found was that

Most reports of green tomatoes being toxic are entirely based on their being part of Solanum and therefore containing solanine, not on any real case reports of someone getting sick (nearly all examples of someone getting sick that I read about were from potatoes [not tomatoes] that had turned green)

Technically, in tomatoes, it isn't even solanine, but rather a related compound called tomatine, which is produced.

There has been no reports of tomatine causing illnesses, and some reports on tomatine's beneficial properties (including reducing cholesterol)

You may even be able to eat the leaves of tomato plants safely

Peruvians eat a variety of red tomatoe which has the same tomatine content as green tomatoes, without any apparent ill effects

So, I'm not as worried as I was about my dried green tomatoes, but I'm still not completely convinced they are safe. If anyone knows anything more, please post in the comments.

But that's not the interesting part.

While I was investigating, I cam across this paper on tomato alkaloids. On page 5759 (the 9th page of the PDF) it gives this amazingly interesting fact:

Until the recent discovery of dehydrotomatine, it wasthought that tomatoes contain only one glycoalkaloid, usuallycalled α-tomatine or tomatine. The question arises why eachof the major Solanum plants produced two glycoalkaloids[potatoes, α-chaconine and α-solanine (106); eggplants, solamargineand solasonine (115); tomatoes, dehydrotomatine andα-tomatine].

So to my mind, this brings up several interesting questions:

Why are these glycoalkaloids in pairs?

More importantly, if we assume that these are from an original created kind, how did each one manage to get a different type of glycoalkaloid, and still get exactly two?

Is the usefulness or harmfulness of these substances an intentional part of creation or simply a byproduct of its diversification method?

So, for instance, many of these substances are used medicinally. Is the wide variety of alkaloids there for the purpose of healing, or is that merely something that we've imposed on them? Are the ones that are toxic there for the purpose of harming humans, or is that just a byproduct of how the plant's biochemistry evolved?

The wierd thing, which I think may be key to figuring at least some of this out, is that these alkaloids are evolving in pairs. I think there must be some underlying mutational mechanism which is causing the coordination of the glycoalkaloids. Thus, with a single mechanism, perhaps both compounds can be changed in a coordinated style, to maintain their synergistic reactions (whatever they are), but yet be modified in a way that is useful either to the plant or to others. Perhaps the radiation of glycoalkaloids is stochastic - if it were purely stochastic, then this would possibly give weight to the idea that they were _designed_ for medicinal uses, since this would make sure that all (or nearly all) of the potential glycoalkaloids were available somewhere in creation. If, instead, they were adaptive, then we would probably say that their use to humans is a byproduct and not their reason for existence.

In any case, if I had time, looking into these chemical structures, their gene sequences, and possible mutational mechanisms would make a fun project. Of course, I may need to wait until the Tomato Genome Project is completed.

I had better stop now and get my last batch of dried green tomatoes out of the oven!

Many retroviral env proteins help cells fuse together to form larger complexes

Ty elements in yeast are similar to retroviruses, but lack evn proteins

Solo LTR's can be created by an LTR being inserted during the repair of a double-stranded break (indicating that a solo LTR is not necessarily the result of a ERV deletion)

Viruses can package pieces of host DNA and move it between hosts (known as transduction)

Expressed ERVs prevent infection from similar ERVs

Different retroviruses have different target site preferences

The authors use these and other items to infer that retroviruses were originally part of the genome itself, and were later exogenized into free particles for infection. They also propose that retroviruses were used for horizontally transferring genetic material.

My personal hunch is that retroviruses have neither an origination outside the organism nor inside the originally-created DNA (at least not exclusively). I tend to go with Blanden and Steele's suggestion in Lamarck's Signature that they are instead used for somatic selection. That is, somatic cells do the real evolutionary work, and retroviruses package up that material and transport it - either back to the germ line or to other somatic cells.

Thus, retroviruses are essentially created by (or at least used by) somatic cells to move new genes back to the germ line for more efficient adaptation to new environments.